MolNFT v1 · #116505 · protein
Crystal structure of spider monkey cytochrome C at 1.15 ångström
5DFS: “Crystal structure of spider monkey cytochrome C at 1.15 ångström”. X-ray diffraction, 2 ligands (HEC, CL), 2 pockets (best druggability 0.79). MolNFT v1 #116505 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DFS
- Type
- protein
- Length
- 208 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C
- UniProt
- P00003
- Ligands
- HEC, CL
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome C | protein | 104 | 42% helix, 2% strand | P00003 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.79 | 0.91 | 48 | HEC |
| 2 | 191 | 0.76 | 0.91 | 34 | HEC |
Interfaces
1 interface between chains.
- A–B · 435 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00003
- Elsewhere: RCSB PDB 5DFS · PDBe 5DFS · UniProt P00003
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